scFFPE-ATAC, single-cell chromatin accessibility in formalin-fixed paraffin-embedded samples, is published in Nature Communications.

Congratualtons to Ram and Pengwei.

We're excited to announce that our team at Uppsala University has developed scFFPE-ATAC, the first-ever method to profile  (FFPE) tissues—some as old as 13 years!

FFPE samples are the backbone of clinical pathology, with hundreds of millions to over a billion stored in hospitals and research centers globally. Yet despite their importance, these priceless archives have remained largely off-limits to modern single-cell epigenomic tools.

Why scFFPE-ATAC matters:

• Recovers epigenetic information from highly damaged, archived tissue

• Works on decade-old FFPE samples

• Enables single-cell resolution of chromatin regulation in cells from tumors, lymph nodes, and more

• Reveals critical differences in regulatory programs between tumor center and invasive edge

• Uncovers epigenetic changes associated with cancer relapse and transformation

🧪 In our study, we validated scFFPE-ATAC in mouse spleen, human lymph nodes (8–12 years old), lung cancer tissues, and paired lymphoma samples from diagnosis and relapse/transformation.

💡 This technology opens the door for retrospective, spatial, and mechanistic epigenetic studies using archived clinical specimens—and has the potential to drive major breakthroughs in cancer research, disease progression, and personalized medicine.

📄 Read the full paper here: https://www.nature.com/articles/s41467-025-66170-4 

A huge thank-you to all collaborators and funding bodies (Knut and Alice Wallenberg foundation, Swedish research council and Swedish Cancer Society) who made this possible. We’re thrilled about the new research pathways that scFFPE-ATAC will unlock—and eager to see how the community applies it next.